Working on a 2003 Element, 2.4 liter, 4wd. The charging system is non-op. It has a new, fully charged battery, clean, tight cables, all fuses check good, disconnected the 4 wire connector at the alternator and with the key on, one wire has 12.2 v. Normally I would just replace the alternator BUT, the charge warning lamp on the dash is out, won't even come on during the initial start bulb check. My question is---will this affect the charge output of the alternator? I cannot find much info online about this system. Any info would be appreciated, Thanks!

The charging warning lamp not coming on won't affect the alternator's output. Remember, the regulated battery output should be 14 to 15 volts across the battery terminals, with the engine idling. If it's low, replace the alternator. Most auto parts stores will test alternators for free.

Ensure you tested all under hood and under dash fuses with a test light or multi-meter. Clean the connections going to the alternator and the "B" wire. If there's a "mega fuse," between the B wire and the battery, make sure the connections are clean and the fuse has not blown.

The charging warning lamp not coming on won't affect the alternator's output. Remember, the regulated battery output should be 14 to 15 volts across the battery terminals, with the engine idling. If it's low, replace the alternator.

Ensure you tested all under hood and under dash fuses with a test light or multi-meter.
I didn't find much information online about this car concerning the charging system, but I do remember some of the earlier Honda's had a dash problem with a regulator that would short and it was part of the charge gauge system, causing a no-charge situation along with 3 separate fusible links and 2 fuses that could stop the alternator from charging as well. Thanks for the info!
This is a new Mom and Pop shop I work at, and they don't have Mitchell or Alldata, so I have to go by experience and common sense.